Reduced greenhouse gas emissions via improved energy efficiency represents the ultimate challenge for the energy economy of the future. In this context, fuel cells for power generation aboard aircrafts have a promising potential to effectively contribute to the greening of air transportation. They can simplify today’s aircraft comprising electric, pneumatic and hydraulic systems towards a more electric airplane. Although they are not considered in the short term as an alternative propulsion system for commercial aviation, many efforts are being devoted to their use as auxiliary power units and even aiming to build a distributed power network that might alleviate duties of the engine driven generators. In addition they allow new functions as zero emission during taxiing on ground and /or increase safety by replacing the emergency ram air turbine (RAT) by a fuel cell based emergency power generator. The present paper focuses on the effort that Compan˜i´a Espan˜ola de Sistemas Aerona´uticos (CESA) is putting into the development of an aeronautical fuel cell system based on a high temperature PEMFC covering all aspects from fundamental research in materials & processes to final integration concepts as a function of different architectures. A great deal of time and effort has been invested to overcome the challenges of PEM fuel cell operation at high temperatures. Among the advantages of these systems are the enhancement of electrochemical kinetics, simplification of water management and cooling, recovery of wasted heat and the possibility of utilizing reformed hydrogen thanks to higher tolerance to impurities. However, new problems arise with the high temperature concept that must be addressed like structural and chemical degradation of materials at elevated temperatures. One of the aeronautical applications where a fuel cell has an important role to play in the short term is the emergency power unit. Weight and mechanical complexity of traditional ram air turbines could be drastically reduced by the introduction of a hydrogen fueled system. In addition, the output of the fuel cell is aircraft’s speed independent. This means additional power supply in case of emergency allowing a safer landing of the aircraft. However, a RAT replacement must overcome the specific difficulties concerning the very short start-up times allowed and the heating/cooling strategies to quickly raise the temperature to elevated levels and accurately maintaining the optimum operating range once in service.